RetrogeneDB ID: retro_mdom_1979

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:36495654..36496078(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010191
• Aliases: None
• Description: None

Sequence

>retro_mdom_1979
GTCTCCAAAGGAGTTAAAGTTCCACATAATTTTCACTTGTTAGAAGAACTTGAAGAAGACCAAAAAAGGAGTAGGCTTTT
TTAGCTGGGGACTTGAAGACGATGAAGATATGACACTTACAAGGTGGACAGGCATGATTATTGGGCCACCAAGGACAAAC
TATGAAAACAGAATATACAGTCTGAAAGTAGAGTGTGGACCTTAAATACCCAGAAGCACCTCCAACAGTTAGATTTGTAA
CAAAAATTAATATGAATGGGATAAATAATTCTAATGGAATGGTAGATGCAAGGAAAATACCAGTATTAGCAAAATGGCAA
AATTTTTATAGCATTAAAGTTGTACTTCAAGAGCTAAGGTGTCTAATGATGTCCAAAGAAAACATGAAGCTTCCCCACCT
CCAAAAGGATAAACATACAGCAGT

Alignment

ORF - retro_mdom_1979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.67 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSTGVKVPRNFRLLEELEEGQ-KGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGP
          VS.GVKVP.NF.LLEELEE.Q.KGVG....SWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGP
Retrocopy VSKGVKVPHNFHLLEELEEDQ>KGVG--FFSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGP

Parental  -KYPEAPPTVRFVTKINMNGINNSNGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQ-PPE
          .KYPEAPPTVRFVTKINMNGINNSNGMVDAR.IPVLAKWQN.YSIKVVLQELR.LMMSKENMKLP..PP.
Retrocopy >KYPEAPPTVRFVTKINMNGINNSNGMVDARKIPVLAKWQNFYSIKVVLQELRCLMMSKENMKLPH<PPK

Parental  GQTYSN
          G.TYS.
Retrocopy G*TYSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1979 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1979 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023218	1 retrocopy	retro_btau_902,
Canis familiaris	ENSCAFG00000028827	1 retrocopy	retro_cfam_1223,
Callithrix jacchus	ENSCJAG00000032182	1 retrocopy	retro_cjac_814,
Cavia porcellus	ENSCPOG00000014413	4 retrocopies	retro_cpor_1277, retro_cpor_540, retro_cpor_751, retro_cpor_849,
Felis catus	ENSFCAG00000007602	6 retrocopies	retro_fcat_1169, retro_fcat_1256, retro_fcat_141, retro_fcat_15, retro_fcat_1678, retro_fcat_1868,
Loxodonta africana	ENSLAFG00000017749	1 retrocopy	retro_lafr_1168,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Myotis lucifugus	ENSMLUG00000002057	6 retrocopies	retro_mluc_1077, retro_mluc_2371, retro_mluc_386, retro_mluc_559, retro_mluc_659, retro_mluc_985,
Macaca mulatta	ENSMMUG00000008223	1 retrocopy	retro_mmul_1066,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979 , retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mustela putorius furo	ENSMPUG00000001010	2 retrocopies	retro_mputfur_460, retro_mputfur_979,
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048, retro_mmus_2770,
Nomascus leucogenys	ENSNLEG00000013382	1 retrocopy	retro_nleu_1671,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Procavia capensis	ENSPCAG00000000293	1 retrocopy	retro_pcap_138,
Pongo abelii	ENSPPYG00000018575	1 retrocopy	retro_pabe_2739,
Rattus norvegicus	ENSRNOG00000001829	1 retrocopy	retro_rnor_1181,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524,
Ictidomys tridecemlineatus	ENSSTOG00000021769	2 retrocopies	retro_itri_568, retro_itri_900,
Tupaia belangeri	ENSTBEG00000015720	27 retrocopies	retro_tbel_1333, retro_tbel_1456, retro_tbel_1479, retro_tbel_1551, retro_tbel_160, retro_tbel_1740, retro_tbel_1784, retro_tbel_2129, retro_tbel_2149, retro_tbel_2317, retro_tbel_2334, retro_tbel_2496, retro_tbel_2890, retro_tbel_2935, retro_tbel_3021, retro_tbel_3102, retro_tbel_3141, retro_tbel_3461, retro_tbel_3573, retro_tbel_3734, retro_tbel_3935, retro_tbel_3971, retro_tbel_4227, retro_tbel_4319, retro_tbel_4720, retro_tbel_640, retro_tbel_909,
Tursiops truncatus	ENSTTRG00000008325	1 retrocopy	retro_ttru_1623,